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Nucleo-cytoplasmic mRNA distribution

ABSTRACT: Nuclear and cytoplasmic RNA were extracted by hypotonic cell lysis from D.-mel2 cell knock down by RNAi against dU2AF50 or with non-specific dsRNA. Keywords: other

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE1344 | GEO | 2004/05/01

SECONDARY ACCESSION(S): PRJNA90091

REPOSITORIES: GEO

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RNAi knock down of dU2AF50 in Drosophila mel2 cells and profiling of nuclear and cytoplasmic fractions

Project description:Nuclear and cytoplasmic RNA were extracted by hypotonic cell lysis from D.-mel2 cell knock down by RNAi against dU2AF50 or with non-specific dsRNA.

2007-07-05 | E-GEOD-1344 | biostudies-arrayexpress

Nucleo-cytoplasmic RNA distribution responsible for maintaining neuroinflammatory microenvironment.

Project description:Characteristics of subcellular localization of RNAs are closely associated with their transcriptional outputs and, therefore, involved in the physiological process of many cases of central nervous system diseases, such as hemorrhagic stroke, which threatens millions of people and causes of death and long-term disability world-wide. Using whole-transcriptome sequencing (RNA-seq), here we report a subcellular gene profiling during hemorrhagic damage. Differentially expressed genes owing to spatial distribution of oxyhemoglobin (oxy-hb) treated-microglial nuclear and cytoplasmic fractions were enriched in biological processes in RNA metabolism and RNA splicing regardless of the duration of stimulation; while hemorrhage-induced differentially expressed genes played roles in inflammation regardless of the duration of stimulation. Interestingly, nuclear-retained intron of microglial nucleocytoplasmic transport genes may result in their down-regulation in 24 hours of oxy-Hb stimulation. This transcriptome study advances our understanding of the contributor of subcellular components, revealing new insights into cytoplasmic non-coding RNAs in response to hemorrhage and provide a resource for investigating comparable diseases.

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Analysis of Plasma Membrane, Endosomal and Cytoplasmic fractions of mouse embryonic fibroblast

Project description:This project aimed to identify novel endosomal proteins and therefore cellular fractionation experiments were performed. Adherent mouse embryonic fibroblast were scraped on ice into hypotonic lysis buffer (10 mM HEPES-KOH pH 7.2, 0.25 M sucrose, 1 mM EDTA, 1 mM MgOAc and protease & phosphatase inhibitors (PhosSTOP and Complete mini tablets from Roche). Cell membranes were fragmented with French Press and nuclei removed with 10 min 1000 x g centrifugation. Plasma membrane fraction was collected with 10 min 10 000 x g centrifugation and endosomal/cytoplasmic fractions with 1h 100,000 x g centrifugation. Membrane fractions were washed at least once with lysis buffer and cytoplasmic fractions were centrifuged twice. All fractionation steps were performed at +4°C or on ice. All fractions were dissolved in sample buffer for immunoblotting

2015-10-14 | PXD001870 | Pride

bioadapt2011_cytopheno-CYTOPHENO: Nucleo-cytoplasmic co-adaptation and adaptive plant phenotypes

Project description:The cytopheno project studies cytoplasmic-nucleus interactions by characterizing cytolines (same nucleus but different cytoplasm, and conversely) at several levels (growth, germination, transcriptomic, proteomic, metabolomic) notably in response to nitrogen deficiency. For this project, there are 48 hybridizations performed as following, on leaf samples from hydroponically grown plants. bioadapt2011_cytopheno - bioadapt2011_cytopheno - Evaluation of the impact of nucleo-cytoplasmic co-adaptation disruptions on nuclear genome expression in Arabidopsis - Obtaining samples by hydroponic culture.

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The DEAD box helicase RDE-12 promotes amplification of RNAi in cytoplasmic foci in C. elegans

Project description:RNA interference (RNAi) is a potent mechanism for down-regulating gene expression. Conserved RNAi pathway components are found in animals, plants, fungi and other eukaryotes. In C. elegans, the RNAi response is greatly amplified by the synthesis of abundant secondary siRNAs. Exogenous double stranded RNA is processed by Dicer and RDE-1/Argonaute into primary siRNA that guides target mRNA recognition. The RDE-10/RDE-11 complex and the RNA dependent RNA polymerase RRF-1 then engage the target mRNA for secondary siRNA synthesis. However, the molecular link between primary siRNA production and secondary siRNA synthesis remains largely unknown. Furthermore, it is unclear if the sub-cellular sites for target mRNA recognition and degradation coincide with sites where siRNA synthesis and amplification occur. In the C. elegans germline, cytoplasmic P granules at the nuclear pores and perinuclear Mutator foci contribute to target mRNA surveillance and siRNA amplification, respectively. We report that RDE-12, a conserved FG domain containing DEAD-box helicase, localizes in P-granules and cytoplasmic foci that are enriched in RSD-6 but are excluded from the Mutator foci. Our results suggest that RDE-12 promotes secondary siRNA synthesis by orchestrating the recruitment of RDE-10 and RRF-1 to primary siRNA targeted mRNA in distinct cytoplasmic compartments. Examination of exogenous dsRNA trigger derived siRNA in wildtype and rde-12 mutant animals

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Nucleo-cytoplasmic partitioning of ARF proteins controls auxin responses in Arabidopsis thaliana

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Exclusion of NFAT5 from mitotic chromatin resets its nucleo-cytoplasmic distribution in interphase.

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Profiling nucleo/cytoplasmic distribution of mRNAs identifies a role for the Golgi-to-ER trafficking in C9orf72 toxicity

Project description:Compelling evidence indicates that defects in nucleocytoplasmic transport contribute to the pathogenesis of amyotrophic lateral sclerosis (ALS). In particular, hexanucleotide (G4C2) repeat expansions in C9orf72, the most common cause of genetic ALS, have a widespread impact on the transport machinery that regulates the nucleocytoplasmic distribution of proteins and RNAs, thereby affecting their functions. We have previously reported that the expression of G4C2 hexanucleotide repeats in cultured human and mouse cells caused a marked accumulation of poly(A) mRNAs in cell nuclei, suggesting that mRNA trafficking is impaired by expanded C9orf72-ALS repeats. To further characterize the process, in this work we set out to systematically identify the specific mRNAs that are altered in their nucleocytoplasmic distribution in the presence of C9orf72-ALS repeats. Results from RNAseq profiling of nuclear and cytoplasmic RNA fractions obtained from cells expressing G4C231 repeats show a significant accumulation of mRNAs in the nuclei of G4C231 cells, further suggesting that nuclear retention of mRNAs is a major effect of C9orf72 expanded repeats expression. Interestingly, pathway analysis shows that mRNAs involved in ER-to-Golgi trafficking are particularly enriched among the identified mRNAs. Most importantly, functional studies in cultured cells and Drosophila indicate that the membrane trafficking route regulated by ARFGAP1, a GTPase-activating protein that associates with Golgi, is specifically affected by expanded C9orf72 repeats, as well as by C9orf72-related dipeptide repeat proteins (C9-DPRs), pointing to ER-to-Golgi vesicle-mediated transport as a target of C9orf72 toxicity.

2023-08-21 | GSE235448 | GEO

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